Merge pull request #21 from noaa-ocs-modeling/develop

extract jobid from output string and use in job submission dependencies
noaa-ocs-modeling · Feb 17, 2021 · 74f9a67 · 74f9a67
2 parents a893e93 + 4e89e2f
commit 74f9a67
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Showing 6 changed files with 14 additions and 9 deletions.
diff --git a/coupledmodeldriver/job_script.py b/coupledmodeldriver/job_script.py
@@ -418,7 +418,12 @@ def __str__(self) -> str:
         ]
 
         if self.platform != Platform.LOCAL:
-            lines.append('squeue -u $USER -o "%.8A %.4C %.10m %.20E"')
+            # slurm queue output https://slurm.schedmd.com/squeue.html
+            squeue_command = 'squeue -u $USER -o "%.8F %.21j %.4C %.4D %.31E %.7a %.9P %.20V %.20S %.20e"'
+            lines.extend([
+                f'echo {squeue_command}',
+                squeue_command,
+            ])
 
         return '\n'.join(lines)
 
@@ -428,8 +433,8 @@ def coldstart(self) -> str:
         if self.platform != Platform.LOCAL:
             lines.extend(
                 [
-                    'coldstart_adcprep_jobid=$(sbatch adcprep.job)',
-                    'coldstart_jobid=$(sbatch --dependency=afterany:$coldstart_adcprep_jobid nems_adcirc.job)',
+                    "coldstart_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}')",
+                    "coldstart_jobid=$(sbatch --dependency=afterany:$coldstart_adcprep_jobid nems_adcirc.job | awk '{print $NF}')",
                 ]
             )
         else:
@@ -447,7 +452,7 @@ def hotstart(self) -> str:
         if self.platform != Platform.LOCAL:
             lines.extend(
                 [
-                    'hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$coldstart_jobid adcprep.job)',
+                    "hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$coldstart_jobid adcprep.job | awk '{print $NF}')",
                     'sbatch --dependency=afterany:$hotstart_adcprep_jobid nems_adcirc.job',
                 ]
             )

diff --git a/examples/hera/hera_hsofs_irma.py b/examples/hera/hera_hsofs_irma.py
@@ -28,7 +28,7 @@
 OUTPUT_DIRECTORY = (Path(__file__).parent / '../data') / 'configuration' / 'hera_hsofs_irma'
 
 if __name__ == '__main__':
-    runs = {f'nems_hsofs_test': (None, None)}
+    runs = {f'test_case_1': (None, None)}
 
     # init tidal forcing and setup requests
     tidal_forcing = Tides()

diff --git a/examples/hera/hera_hsofs_sandy.py b/examples/hera/hera_hsofs_sandy.py
@@ -28,7 +28,7 @@
 OUTPUT_DIRECTORY = (Path(__file__).parent / '../data') / 'configuration' / 'hera_hsofs_sandy'
 
 if __name__ == '__main__':
-    runs = {f'nems_hsofs_test': (None, None)}
+    runs = {f'test_case_1': (None, None)}
 
     # init tidal forcing and setup requests
     tidal_forcing = Tides()

diff --git a/examples/local/local_hsofs_irma.py b/examples/local/local_hsofs_irma.py
@@ -24,7 +24,7 @@
 OUTPUT_DIRECTORY = (Path(__file__).parent / '../data') / 'configuration' / 'local_hsofs_irma'
 
 if __name__ == '__main__':
-    runs = {f'nems_hsofs_test': (None, None)}
+    runs = {f'test_case_1': (None, None)}
 
     # init tidal forcing and setup requests
     tidal_forcing = Tides()

diff --git a/examples/local/local_hsofs_sandy.py b/examples/local/local_hsofs_sandy.py
@@ -24,7 +24,7 @@
 OUTPUT_DIRECTORY = (Path(__file__).parent / '../data') / 'configuration' / 'local_hsofs_sandy'
 
 if __name__ == '__main__':
-    runs = {f'nems_hsofs_test': (None, None)}
+    runs = {f'test_case_1': (None, None)}
 
     # init tidal forcing and setup requests
     tidal_forcing = Tides()

diff --git a/examples/stampede2/stampede2_hsofs_sandy.py b/examples/stampede2/stampede2_hsofs_sandy.py
@@ -22,7 +22,7 @@
 )
 
 if __name__ == '__main__':
-    runs = {f'nems_hsofs_test': (None, None)}
+    runs = {f'test_case_1': (None, None)}
 
     # init tidal forcing and setup requests
     tidal_forcing = Tides()